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CN-122012743-A - Application of sheep molecular marker combination, chip, kit, method and application

CN122012743ACN 122012743 ACN122012743 ACN 122012743ACN-122012743-A

Abstract

The invention relates to the technical field of molecular detection, and particularly discloses application of sheep molecular marker combinations, a chip, a kit, a method and application, wherein the application comprises colony genetic analysis and economic character prediction of local sheep, the local sheep comprises small-tailed han sheep, yuxi fat-tailed sheep, big-tailed han sheep, taihe fur sheep, homosheep, medium-relaxation mutton sheep and Huang Huai mutton sheep, the sheep molecular marker combinations comprise 12363 SNP sites and 18 Indel sites, the 12363 SNP sites and the 18 Indel sites are determined based on whole genome sequence comparison of sheep reference genome, the version number of the whole genome sequence of the sheep reference genome is ARS-UI_ Ramb _v3.0, the 12363 SNP sites are shown in table 1, and the 18 Indel sites are shown in table 2. The invention can be used for population genetics analysis and economic character prediction of local sheep.

Inventors

  • SHI HUIBIN
  • LI JUN
  • LIU KUN
  • HAN HAOYUAN
  • QUAN KAI
  • WEI CAIHONG
  • WANG HUIHUA
  • JIN MEILIN

Assignees

  • 河南牧业经济学院

Dates

Publication Date
20260512
Application Date
20260324

Claims (15)

  1. 1. The application of the sheep molecular marker combination is characterized in that the application comprises colony genetic analysis and economic character prediction of local sheep, wherein the local sheep comprises small-tailed han sheep, yuxi-fat-tailed sheep, large-tailed han sheep, taihe fur sheep, homosheep, medium-relaxation mutton sheep and Huang-Huai mutton sheep, the sheep molecular marker combination comprises 12363 SNP sites and 18 Indel sites, the 12363 SNP sites and the 18 Indel sites are determined based on whole genome sequence alignment of sheep reference genome, the version number of the whole genome sequence of the sheep reference genome is ARS-UI_ Ramb _v3.0, the 12363 SNP sites are shown in table 1, and the 18 Indel sites are shown in table 2: TABLE 1 TABLE 2 。
  2. 2. A sheep low-density 10K liquid phase chip, wherein genotyping of the sheep low-density 10K liquid phase chip comprises 12363 SNP sites and 18 Indel sites according to claim 1.
  3. 3. The sheep low density 10K liquid phase chip according to claim 2 further comprising probes designed according to the gene sequences covering 12363 SNP sites and 18 Indel sites.
  4. 4. A sheep low density 10K liquid phase chip according to claim 3, characterized in that the GC content ratio of the probe sequences is 30-70%, the probe length is 110bp, the highest upper limit of the number of specific similar fragments on the reference genome is less than 5, the maximum distance from the designed region is less than 10bp.
  5. 5. A kit comprising the sheep low density 10K liquid phase chip of claim 3 or 4 or comprising probes and/or primers for detecting 12363 SNP sites as set forth in table 1 and 18 Indel sites as set forth in table 2.
  6. 6. The method for designing a sheep low density 10K liquid phase chip according to claim 3 or 4, comprising the steps of: S1, obtaining high-quality SNP loci: s11, collecting samples, namely obtaining DNA samples of local sheep, wherein the local sheep comprises small tail cold sheep, yuxi fat tail sheep, large tail cold sheep, taihe fur sheep, sheep and medium-relaxation mutton sheep; S12, acquiring an original SNP locus, namely carrying out whole genome re-sequencing on the DNA sample to obtain the original SNP locus; s13, data quality control and comparison, namely comparing the original SNP locus to a sheep reference genome, and performing quality control filtration to obtain a high-quality SNP locus; S2, screening variety specific loci, namely calculating absolute difference delta RAF of allele frequencies among varieties, sequencing from high to low according to delta RAF values, and finally screening 805 specific SNP loci which are most remarkably differentiated among varieties from the high-quality SNP loci obtained in the step S13; S3, screening functional sites: S31, acquiring phenotype data related to economic traits of local sheep samples and sheep in the step S11, and performing quality control; S32, carrying out GWAS analysis on the high-quality SNP loci obtained in the step S13 and the phenotype data obtained after quality control in the step 21, respectively screening candidate SNP loci of each economic trait based on correlation significance, and then removing redundancy to obtain 3534 functional SNP loci which are obviously related to important economic traits; S4, screening sheep 1K loci, namely screening high-quality loci obtained in the step S13 by adopting GenoBaits cube sheep 1K liquid phase chips, and totally screening 1510 SNP loci and 18 Indel loci; s5, screening background sites: screening SNP loci obtained through sheep reference genome comparison screening to obtain 7334 background SNP loci; S6, combining 805 specific SNP loci, 3534 functional SNP loci, 1510 SNP loci and 7334 background SNP loci, removing duplication and optimizing to finally obtain 12363 SNP loci and 18 Indel loci.
  7. 7. The design method according to claim 6, wherein in step S13, the condition of quality control filtering includes: the lowest sequencing depth is less than 2X, the site deletion rate is more than 10% and the minor allele frequency is less than or equal to 0.05.
  8. 8. The method of designing according to claim 6, wherein in step S21, the sheep economic traits include birth weight, weaning weight, 6 month old body height, 6 month old body length, 6 month old circumference and 6 month old chest width.
  9. 9. The method according to claim 6, wherein in step S5, the screening conditions include: a low sequencing depth of 5X or more, a deletion rate of less than 0.1 and a MAF of greater than 0.05.
  10. 10. Use of the sheep low density 10K liquid phase chip of claim 3 or 4 for local sheep genotyping.
  11. 11. Use of the sheep low-density 10K liquid chip according to claim 3 or 4 for local sheep genetic diversity analysis, population structure analysis, genetic relationship identification or breed identification.
  12. 12. Use of a sheep low density 10K liquid phase chip according to claim 3 or 4 in the prediction of local sheep economic shapes including birth weight, weaning weight, weight at 6 months of age, body length at 6 months of age, tube circumference at 6 months of age and chest width at 6 months of age.
  13. 13. Use of the kit according to claim 5 for genotyping local sheep.
  14. 14. Use of the kit according to claim 5 for local sheep genetic diversity analysis, population structure analysis, genetic relationship identification or breed identification.
  15. 15. Use of the kit according to claim 5 for predicting the economic shape of a local sheep, wherein the economic shape of a local sheep comprises birth weight, weaning weight, 6 month old body height, 6 month old body length, 6 month old circumference and 6 month old chest width.

Description

Application of sheep molecular marker combination, chip, kit, method and application Technical Field The invention relates to the technical field of molecular detection, in particular to application of sheep molecular marker combination, a chip, a kit, a method and application. Background With the continuous development of the global livestock industry, sheep serve as important economic animals, and research and utilization of genetic resources of sheep are increasingly emphasized. The sheep stock quantity, the sheep output quantity and the mutton output quantity of China all stay the first place in the world. Henan province is used as a major province of agriculture and animal husbandry, has rich sheep and goat variety resources, and is one of main producing areas of five large mutton sheep in China. Four main sheep species are small tailed han sheep, yuxi fat tailed sheep, large tailed han sheep and Taihe fur sheep in Henan province. The Huang-Huai mutton sheep and the Zhong-Yu mutton sheep are bred by taking the small-tailed han sheep as a female parent, wherein the Huang-Huai mutton sheep is a new mutton sheep variety which is first examined by China in Henan province and has the characteristics of high breeding rate, high growth speed, coarse feeding resistance, good meat quality and the like, and the main production performance of the Huang-Huai mutton sheep reaches the international advanced level, and has remarkable popularization and application values. The local sheep genetic resource is precious breeding material, and the protection and development of the local sheep genetic resource are important to the excavation of high-quality germplasm genes and the genetic improvement plan of livestock and poultry. With the continuous development of the industry, the germplasm characteristics of sheep in deep mining places are scientifically evaluated, developed and utilized, and the precise evaluation of molecular level is required to be changed. In the genome breeding age, the application of the genome breeding chip can effectively identify the flocks carrying specific genes, thereby accelerating the breeding of excellent varieties. The shortage of Henan province in local sheep genome research and chip development makes the current breeding technology still mainly adopt traditional means, mainly relies on artificial experience and appearance characteristic evaluation, and leads to slow breeding progress. Therefore, the development of the gene chip suitable for the local sheep population in Henan province not only promotes the genetic improvement level of sheep and promotes the sustainable development of animal husbandry, but also provides scientific basis for the protection, development and utilization of local sheep varieties and solid guarantee for the happiness of the sheep species in Henan province. Disclosure of Invention The invention aims to provide application of sheep molecular marker combination, a chip, a kit, a method and application, and can be used for population genetic analysis and economic character prediction of local sheep. The invention is realized by the following technical scheme: The application of the sheep molecular marker combination comprises colony genetic analysis and economic character prediction of local sheep, wherein the local sheep comprises Henan local sheep and Shaanxi local sheep, specifically, the local sheep comprises small tail cold sheep, yuxi fat tail sheep, big tail cold sheep, taihe fur sheep, huang Huai sheep and Zhongyu sheep, the sheep molecular marker combination comprises 12363 SNP sites and 18 Indel sites, the 12363 SNP sites and the 18 Indel sites are determined based on the whole genome sequence comparison of sheep reference genome, the version number of the whole genome sequence of the sheep reference genome is ARS-UI_ Ramb _v3.0, the 12363 SNP sites are shown in table 1, and the 18 Indel sites are shown in table 2: TABLE 1 ; Note that the numbers before "_" in Table 1 indicate chromosomes, and the numbers after "_indicate specific positions on the corresponding chromosomes. TABLE 2 Wherein the numbers preceding "_" in the physical locations represent the chromosomes and the numbers following "_" represent the physical locations of the sites on the corresponding chromosomes. Wherein, the genetic analysis of the population comprises genetic diversity analysis, population structure analysis, genetic relationship identification and variety identification of sheep, and the economic characters comprise birth weight, weaning weight, 6 month age height, 6 month age body length, 6 month age tube circumference and 6 month age chest width. The 12363 SNP loci and the 18 Indel loci are obtained by carrying out whole genome re-sequencing, variety specificity locus screening, GWAS analysis and screening on samples of 5 local sheep varieties (small tail han sheep, yuxi fat tail sheep, large tail han sheep, taihe fur sheep and sheep), and the obtained 12363 SNP loci an